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And now some updates for SDY readers from the Editor…. 现在编辑为SDY读者提供一些更新....
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-05-01 DOI: 10.1063/4.0000198
George N Phillips
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引用次数: 0
Structural biology and public health response to biomedical threats. 结构生物学和公共卫生应对生物医学威胁。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-05-01 DOI: 10.1063/4.0000186
Joanna Lenkiewicz, Vanessa Bijak, Shrisha Poonuganti, Michal Szczygiel, Michal Gucwa, Krzysztof Murzyn, Wladek Minor

Over the course of the pandemic caused by SARS-CoV-2, structural biologists have worked hand in hand with groups developing vaccines and treatments. However, relying solely on in vitro and clinical studies may be insufficient to guide vaccination and treatment developments, and other healthcare policies during virus mutations or peaks in infections and fatalities. Therefore, it is crucial to track statistical data related to the number of infections, deaths, and vaccinations in specific regions and present it in an easy-to-understand way.

在SARS-CoV-2引起的大流行期间,结构生物学家与开发疫苗和治疗方法的团队携手合作。然而,仅仅依靠体外和临床研究可能不足以在病毒突变或感染和死亡高峰期间指导疫苗接种和治疗发展以及其他卫生保健政策。因此,至关重要的是跟踪与特定区域的感染、死亡和疫苗接种数量有关的统计数据,并以易于理解的方式提供这些数据。
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引用次数: 1
Projection to extract the perpendicular component (PEPC) method for extracting kinetics from time-resolved data. 投影提取垂直分量(PEPC)方法从时间分辨数据中提取动力学。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-05-01 DOI: 10.1063/4.0000189
H Ki, J Gu, Y Cha, K W Lee, H Ihee

Time-resolved x-ray liquidography (TRXL) is a potent method for investigating the structural dynamics of chemical and biological reactions in the liquid phase. It has enabled the extraction of detailed structural aspects of various dynamic processes, the molecular structures of intermediates, and kinetics of reactions across a wide range of systems, from small molecules to proteins and nanoparticles. Proper data analysis is key to extracting the information of the kinetics and structural dynamics of the studied system encrypted in the TRXL data. In typical TRXL data, the signals from solute scattering, solvent scattering, and solute-solvent cross scattering are mixed in the q-space, and the solute kinetics and solvent hydrodynamics are mixed in the time domain, thus complicating the data analysis. Various methods developed so far generally require prior knowledge of the molecular structures of candidate species involved in the reaction. Because such information is often unavailable, a typical data analysis often involves tedious trial and error. To remedy this situation, we have developed a method named projection to extract the perpendicular component (PEPC), capable of removing the contribution of solvent kinetics from TRXL data. The resulting data then contain only the solute kinetics, and, thus, the solute kinetics can be easily determined. Once the solute kinetics is determined, the subsequent data analysis to extract the structural information can be performed with drastically improved convenience. The application of the PEPC method is demonstrated with TRXL data from the photochemistry of two molecular systems: [Au(CN)2-]3 in water and CHI3 in cyclohexane.

时间分辨x射线液相学(TRXL)是研究液相中化学和生物反应结构动力学的一种有效方法。它能够提取各种动态过程的详细结构方面,中间体的分子结构,以及从小分子到蛋白质和纳米颗粒的各种系统的反应动力学。正确的数据分析是提取TRXL数据中加密的所研究系统的动力学和结构动力学信息的关键。在典型的TRXL数据中,溶质散射、溶剂散射和溶质-溶剂交叉散射信号在q空间中混合,溶质动力学和溶剂流体动力学在时域中混合,使数据分析变得复杂。迄今为止开发的各种方法通常需要事先了解参与反应的候选物种的分子结构。由于这些信息通常是不可获得的,因此典型的数据分析通常涉及繁琐的试验和错误。为了纠正这种情况,我们开发了一种名为投影的方法来提取垂直分量(PEPC),能够从TRXL数据中去除溶剂动力学的影响。所得数据只包含溶质动力学,因此,溶质动力学可以很容易地确定。一旦确定了溶质动力学,随后的数据分析以提取结构信息可以大大提高方便进行。用水中的[Au(CN)2-]3和环己烷中的CHI3两种分子体系的TRXL光化学数据证明了PEPC方法的应用。
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引用次数: 1
In crystallo observation of active site dynamics and transient metal ion binding within DNA polymerases. DNA聚合酶活性位点动力学和瞬态金属离子结合的结晶观察。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-05-01 DOI: 10.1063/4.0000187
Caleb Chang, Grace Zhou, Yang Gao

DNA polymerases are the enzymatic catalysts that synthesize DNA during DNA replication and repair. Kinetic studies and x-ray crystallography have uncovered the overall kinetic pathway and led to a two-metal-ion dependent catalytic mechanism. Diffusion-based time-resolved crystallography has permitted the visualization of the catalytic reaction at atomic resolution and made it possible to capture transient events and metal ion binding that have eluded static polymerase structures. This review discusses past static structures and recent time-resolved structures that emphasize the crucial importance of primer alignment and different metal ions binding during catalysis and substrate discrimination.

DNA聚合酶是在DNA复制和修复过程中合成DNA的酶促催化剂。动力学研究和x射线晶体学揭示了整个动力学途径,并导致了双金属离子依赖的催化机制。基于扩散的时间分辨晶体学允许在原子分辨率上可视化催化反应,并使捕获暂时事件和金属离子结合成为可能,这些事件和金属离子结合逃避了静态聚合酶结构。这篇综述讨论了过去的静态结构和最近的时间分辨结构,强调了在催化和底物识别过程中引物排列和不同金属离子结合的重要性。
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引用次数: 0
Pump-probe x-ray microscopy of photo-induced magnetization dynamics at MHz repetition rates. 在MHz重复率下光诱导磁化动力学的泵-探针x射线显微镜。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-03-01 DOI: 10.1063/4.0000167
Kathinka Gerlinger, Bastian Pfau, Martin Hennecke, Lisa-Marie Kern, Ingo Will, Tino Noll, Markus Weigand, Joachim Gräfe, Nick Träger, Michael Schneider, Christian M Günther, Dieter Engel, Gisela Schütz, Stefan Eisebitt

We present time-resolved scanning x-ray microscopy measurements with picosecond photo-excitation via a tailored infrared pump laser at a scanning transmission x-ray microscope. Specifically, we image the laser-induced demagnetization and remagnetization of thin ferrimagnetic GdFe films proceeding on a few nanoseconds timescale. Controlling the heat load on the sample via additional reflector and heatsink layers allows us to conduct destruction-free measurements at a repetition rate of 50 MHz. Near-field enhancement of the photo-excitation and controlled annealing effects lead to laterally heterogeneous magnetization dynamics which we trace with 30 nm spatial resolution. Our work opens new opportunities to study photo-induced dynamics on the nanometer scale, with access to picosecond to nanosecond time scales, which is of technological relevance, especially in the field of magnetism.

我们提出了时间分辨扫描x射线显微镜测量皮秒光激发通过一个定制的红外泵浦激光器在扫描透射x射线显微镜。具体来说,我们在几纳秒的时间尺度上成像了激光诱导的铁磁GdFe薄膜的退磁和再磁化过程。通过额外的反射器和散热器层控制样品的热负荷,使我们能够以50 MHz的重复率进行无破坏的测量。光激发和受控退火效应的近场增强导致了横向非均匀磁化动力学,我们用30 nm的空间分辨率追踪了这一动态。我们的工作为在纳米尺度上研究光致动力学开辟了新的机会,具有皮秒到纳秒的时间尺度,这是技术相关的,特别是在磁性领域。
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引用次数: 1
Deep mining of the protein energy landscape. 深层挖掘蛋白质能源景观。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-03-01 DOI: 10.1063/4.0000180
A Joshua Wand

For over half a century, it has been known that protein molecules naturally undergo extensive structural fluctuations, and that these internal motions are intimately related to their functional properties. The energy landscape view has provided a powerful framework for describing the various physical states that proteins visit during their lifetimes. This Perspective focuses on the commonly neglected and often disparaged axis of the protein energy landscape: entropy. Initially seen largely as a barrier to functionally relevant states of protein molecules, it has recently become clear that proteins retain considerable conformational entropy in the "native" state, and that this entropy can and often does contribute significantly to the free energy of fundamental protein properties, processes, and functions. NMR spectroscopy, molecular dynamics simulations, and emerging crystallographic views have matured in parallel to illuminate dynamic disorder of the "ground state" of proteins and their importance in not only transiting between biologically interesting structures but also greatly influencing their stability, cooperativity, and contribution to critical properties such as allostery.

半个多世纪以来,人们已经知道蛋白质分子自然地经历了广泛的结构波动,这些内部运动与它们的功能特性密切相关。能量景观观点为描述蛋白质在其生命周期中所经历的各种物理状态提供了一个强有力的框架。这个视角关注的是蛋白质能量格局中通常被忽视和经常被贬低的轴:熵。最初主要被视为蛋白质分子功能相关状态的障碍,最近变得清楚的是,蛋白质在“天然”状态下保留了相当大的构象熵,并且这种熵可以并且经常对基本蛋白质性质,过程和功能的自由能做出重大贡献。核磁共振波谱、分子动力学模拟和新兴的晶体学观点已经同步成熟,它们阐明了蛋白质“基态”的动态无序性,以及它们不仅在生物学上有趣的结构之间转移,而且还极大地影响了它们的稳定性、协同性和对变构等关键性质的贡献。
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引用次数: 0
Molecular size dependence on achievable resolution from XFEL single-particle 3D reconstruction. 分子大小依赖于可实现的分辨率从XFEL单粒子三维重建。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-03-01 DOI: 10.1063/4.0000175
Miki Nakano, Osamu Miyashita, Florence Tama

Single-particle analysis using x-ray free-electron lasers (XFELs) is a novel method for obtaining structural information of samples in a state close to nature. In particular, it is suitable for observing the inner structure of large biomolecules by taking advantage of the high transmittance of x-rays. However, systematic studies on the resolution achievable for large molecules are lacking. In this study, the molecular size dependence of the resolution of a three-dimensional (3D) structure resulting from XFEL single-particle reconstruction is evaluated using synthetic data. Evidently, 3D structures of larger molecules can be restored with higher detail (defined relative to the molecular sizes) than smaller ones; however, reconstruction with high absolute resolution (defined in nm-1) is challenging. Our results provide useful information for the experimental design of 3D structure reconstruction using coherent x-ray diffraction patterns of single-particles.

利用x射线自由电子激光器(XFELs)进行单粒子分析是一种获取接近自然状态下样品结构信息的新方法。尤其适合利用x射线的高透射率来观察大分子的内部结构。然而,对于大分子的分辨率还缺乏系统的研究。在这项研究中,利用合成数据评估了由XFEL单粒子重建产生的三维(3D)结构分辨率的分子大小依赖性。显然,与小分子相比,大分子的三维结构可以以更高的细节(相对于分子大小的定义)得到恢复;然而,具有高绝对分辨率(以nm-1定义)的重建是具有挑战性的。我们的结果为单粒子相干x射线衍射图重建三维结构的实验设计提供了有用的信息。
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引用次数: 0
Protein dynamics: The future is bright and complicated! 蛋白质动力学:未来是光明而复杂的!
IF 2.3 2区 物理与天体物理 Q3 CHEMISTRY, PHYSICAL Pub Date : 2023-02-27 eCollection Date: 2023-01-01 DOI: 10.1063/4.0000179
Kwangho Nam, Magnus Wolf-Watz

Biological life depends on motion, and this manifests itself in proteins that display motion over a formidable range of time scales spanning from femtoseconds vibrations of atoms at enzymatic transition states, all the way to slow domain motions occurring on micro to milliseconds. An outstanding challenge in contemporary biophysics and structural biology is a quantitative understanding of the linkages among protein structure, dynamics, and function. These linkages are becoming increasingly explorable due to conceptual and methodological advances. In this Perspective article, we will point toward future directions of the field of protein dynamics with an emphasis on enzymes. Research questions in the field are becoming increasingly complex such as the mechanistic understanding of high-order interaction networks in allosteric signal propagation through a protein matrix, or the connection between local and collective motions. In analogy to the solution to the "protein folding problem," we argue that the way forward to understanding these and other important questions lies in the successful integration of experiment and computation, while utilizing the present rapid expansion of sequence and structure space. Looking forward, the future is bright, and we are in a period where we are on the doorstep to, at least in part, comprehend the importance of dynamics for biological function.

生物生命依赖于运动,这表现在蛋白质中,这些蛋白质在一系列强大的时间尺度上表现出运动,从原子在酶促过渡状态下的飞秒振动,一直到发生在微米到毫秒之间的慢域运动。当代生物物理学和结构生物学的一个突出挑战是定量理解蛋白质结构、动力学和功能之间的联系。由于概念和方法的进步,这些联系正变得越来越可探索。在这篇透视文章中,我们将指出蛋白质动力学领域的未来方向,重点是酶。该领域的研究问题越来越复杂,例如对变构信号通过蛋白质基质传播的高阶相互作用网络的机制理解,或者局部运动和集体运动之间的联系。与“蛋白质折叠问题”的解决方案类似,我们认为,理解这些和其他重要问题的方法在于成功地整合实验和计算,同时利用目前序列和结构空间的快速扩展。展望未来,未来是光明的,我们正处于这样一个时期,至少在一定程度上,我们即将理解动力学对生物功能的重要性。
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引用次数: 0
Biological function investigated by time-resolved structure determination. 通过时间分辨结构测定研究生物功能。
IF 2.8 2区 物理与天体物理 Q1 Physics and Astronomy Pub Date : 2023-02-21 eCollection Date: 2023-01-01 DOI: 10.1063/4.0000177
Marius Schmidt

Inspired by recent progress in time-resolved x-ray crystallography and the adoption of time-resolution by cryo-electronmicroscopy, this article enumerates several approaches developed to become bigger/smaller, faster, and better to gain new insight into the molecular mechanisms of life. This is illustrated by examples where chemical and physical stimuli spawn biological responses on various length and time-scales, from fractions of Ångströms to micro-meters and from femtoseconds to hours.

受时间分辨 X 射线晶体学和低温电子显微镜采用时间分辨技术的最新进展的启发,本文列举了为更大/更小、更快、更好地深入了解生命分子机制而开发的几种方法。本文举例说明了化学和物理刺激在不同长度和时间尺度(从几分之一埃到微米,从飞秒到几小时)催生生物反应的情况。
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引用次数: 0
Solution characterization of the dynamic conjugative entry exclusion protein TraG. 动态共轭入口排斥蛋白 TraG 的溶液特征。
IF 2.3 2区 物理与天体物理 Q3 CHEMISTRY, PHYSICAL Pub Date : 2022-12-27 eCollection Date: 2022-11-01 DOI: 10.1063/4.0000171
Nicholas Bragagnolo, Gerald F Audette

The R100 plasmid and the secretion system it encodes are representative of F-like conjugative type IV secretion systems for the transmission of mobile DNA elements in gram-negative bacteria, serving as a major contributor to the spread of antibiotic resistance in bacterial pathogens. The TraG protein of F-like systems consists of a membrane-bound N-terminal domain and a periplasmic C-terminal domain, denoted TraG*. TraG* is essential in preventing redundant DNA transfer through a process termed entry exclusion. In the donor cell, it interacts with TraN to facilitate mating pair stabilization; however, if a mating pore forms between bacteria with identical plasmids, TraG* interacts with its cognate TraS in the inner membrane of the recipient bacterium to prevent redundant donor-donor conjugation. Structural studies of TraG* from the R100 plasmid have revealed the presence of a dynamic region between the N- and C-terminal domains of TraG. Thermofluor, circular dichroism, collision-induced unfolding-mass spectrometry, and size exclusion chromatography linked to multiangle light scattering and small angle x-ray scattering experiments indicated an N-terminal truncation mutant displayed higher stability and less disordered content relative to full-length TraG*. The 45 N-terminal residues of TraG* are hypothesized to serve as part of a flexible linker between the two independently functioning domains.

R100 质粒及其编码的分泌系统是革兰氏阴性细菌中传播移动 DNA 元素的 F 类共轭 IV 型分泌系统的代表,是细菌病原体抗生素耐药性传播的主要因素。F 型系统的 TraG 蛋白由一个膜结合 N 端结构域和一个围质体 C 端结构域(TraG*)组成。TraG* 在通过一种称为 "入口排斥 "的过程防止多余 DNA 转移方面至关重要。在供体细胞中,它与 TraN 相互作用,促进交配对的稳定;但是,如果具有相同质粒的细菌之间形成了交配孔,TraG* 就会与受体细菌内膜上的同源物 TraS 相互作用,防止供体-受体的冗余共轭。对来自 R100 质粒的 TraG* 的结构研究发现,在 TraG 的 N 端和 C 端结构域之间存在一个动态区域。与多角光散射和小角 X 射线散射实验相关联的热荧光、圆二色、碰撞诱导解折质谱法和尺寸排阻色谱法表明,与全长 TraG* 相比,N 端截短突变体显示出更高的稳定性和更少的无序含量。据推测,TraG* 的 45 个 N 端残基是两个独立功能域之间柔性连接体的一部分。
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引用次数: 0
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